Hybrid rice HR180001

ABSTRACT

Plants, seeds and tissue cultures of the hybrid rice HR180001, and methods for producing a rice plant by crossing a rice plant of hybrid rice HR180001 with itself or with another rice plant, such as a plant of another rice variety or rice hybrid, are disclosed.

BACKGROUND

A new and distinctive hybrid rice designated HR180001 is disclosed.

Rice is an ancient agricultural crop and is today one of the principalfood crops of the world. There are two cultivated species of rice: Oryzasativa L., the Asian rice, and Oryza glaberrima Steud, the African rice.The Asian species constitutes virtually all of the world's cultivatedrice and is the species grown in the United States. Three major riceproducing regions exist in the United States: the Mississippi Delta(Arkansas, Mississippi, northeast Louisiana, southeast Missouri), theGulf Coast (southwest Louisiana, southeast Texas), and the CentralValleys of California. The Gulf Coast and Mississippi Delta regionsmostly use a dry-seeded method of sowing rice whereas; Californiausually uses a water-seeded method.

Rice in the United States is classified into three primary market typesby grain size and shape as: long-grain, medium-grain, and short-grain.Typical U. S. long-grain rice cooks dry and fluffy when steamed orboiled, whereas medium- and short-grain rice cooks moist and sticky.Long-grain cultivars have been traditionally grown in the Southernstates.

Although specific breeding objectives vary somewhat in the differentregions, increasing yield is a primary objective in all programs. Grainyield of rice is determined by the number of panicles per unit area, thenumber of fertile florets per panicle, and grain weight per fertilefloret. Increases in any or all of these yield components provide amechanism to obtain higher yields. Heritable variation exists for all ofthese components, and breeders may directly or indirectly select forincreases in any of them.

The development of uniform hybrid rice requires developing homozygousinbred plants, crossing those inbred plants and evaluating the progenyof those crosses. Pedigree selection, backcross selection, single seedselection, or combinations of these methods are used to develop inbredplants from breeding populations. Those breeding methods combine thegenetic background from two or more inbred plants or various othersources of germplasm, such as, breeding pools from which new inbredplants are developed by selfing, combined with phenotypic or genotypicselection. The new inbred plants are crossed with other inbred plantsand the hybrids created by those crosses are evaluated for commercialpotential. Important commercial traits in hybrid rice may include higheryield, resistance to diseases and insects, herbicide tolerance, betterstems and roots, tolerance to low temperatures, better agronomiccharacteristics, and grain quality.

Each breeding program includes a periodic, objective evaluation of theefficiency of the breeding procedure. Evaluation criteria vary dependingon the goal and objectives, but includes gain from selection per yearbased on comparisons to an appropriate standard, overall value of theadvanced breeding hybrids, and number of successful cultivars producedper unit of input (e.g., per year, per dollar expended, etc.). Promisingadvanced rice hybrids are thoroughly tested and compared to appropriatestandards in environments representative of the commercial targetarea(s) for at least three or more years. The best hybrids arecandidates for new commercial products. These processes, which lead tothe final step of marketing and distribution, usually take from 8 to 12years from the time the first cross is made to develop inbred parentlines, to the subsequent development of improved hybrid rice. Therefore,development of new hybrid rice is a time-consuming process that requiresprecise forward planning, efficient use of resources, and a minimum ofchanges in direction.

A difficult task is the identification of individual plants that aregenetically superior, because for most traits the true genotypic valueis masked by other confounding plant traits or environmental factors.One method of identifying a superior plant is to observe its performancerelative to other experimental plants and to a widely grown standardcultivar. If a single observation is inconclusive, replicatedobservations provide a better estimate of its genetic worth.

Each breeding cycle, the plant breeder selects the germplasm to advanceto the next generation. This germplasm is grown under unique anddifferent geographical, climatic and soil conditions and furtherselections are then made throughout the growing season. The inbred lineswhich are developed are unpredictable. This unpredictability is becausethe breeder's selection occurs in unique environments, with no controlat the DNA level (using conventional breeding procedures), and withmillions of different possible genetic combinations being generated. Abreeder of ordinary skill in the art cannot predict the final resultinghybrids he/she develops, except possibly in a very gross and generalfashion. This unpredictability results in the expenditure of largeamounts of research monies to develop superior new rice cultivars.

Testing is aimed at detecting any major faults and establish the levelof superiority or improvement over current cultivars. In addition toshowing superior performance, there must be a demand for a new cultivarthat is compatible with industry standards or which creates a newmarket. The introduction of a new cultivar will incur additional coststo the seed producer, the grower, processor and consumer; for specialadvertising and marketing, altered seed and commercial productionpractices, and new product utilization. The testing preceding release ofa new cultivar takes into consideration research and development costsas well as technical superiority of the final cultivar. Forseed-propagated cultivars, it is desirable to produce seed easily andeconomically.

Rice, Oryza sativa L., is an important and valuable field crop. Thus, acontinuing goal of rice breeders is to develop stable, high yieldingrice cultivars that are agronomically sound. The reasons for this goalare to maximize the amount of grain produced on the land used and tosupply food for both animals and humans. To accomplish this goal, therice breeder must select and develop rice plants that have the traitsthat result in superior cultivars.

SUMMARY

Disclosed and described are hybrid rice seeds designated HR180001,wherein a representative sample of seed was deposited under ATCCAccession No. PTA-125519, a rice plant, or a part thereof, produced bygrowing the seed, and pollen or an ovule of the plant.

A tissue culture of cells produced from a plant designated HR180001, ora plant part selected from the group consisting of leaves, pollen,embryos, cotyledon, hypocotyl, meristematic cells, roots, root tips,pistils, anthers, flowers, stems, glumes and panicles, and a protoplastproduced from the plant or tissue culture, are also within the scope ofthe disclosure.

A rice plant may be regenerated from the tissue culture, wherein theplant has essentially all of the morphological and physiologicalcharacteristics of hybrid rice HR180001, as listed in Table 1.

A method for producing a hybrid rice seed, includes crossing theHR180001 plant with a different rice plant and harvesting the resultanthybrid rice seed.

A method of producing a herbicide resistant rice plant, includestransforming the rice plant with a transgene, wherein the transgeneconfers tolerance to a herbicide selected from the group consisting ofimidazolinone, cyclohexanedione, sulfonylurea, glyphosate, glufosinate,phenoxy proprionic acid, isoxazole, triketone, L-phosphinothricin,triazine and benzonitrile.

A method of producing an insect resistant rice plant, includestransforming the rice plant with a transgene that confers insectresistance.

A method of producing a rice plant with modified fatty acid metabolismor modified carbohydrate metabolism, include transforming the rice plantwith a transgene encoding a protein selected from the group consistingof fructosyltransferase, levansucrase, alpha-amylase, invertase andstarch branching enzyme and DNA encoding an antisense of stearyl-ACPdesaturase.

A method of introducing one or more desired traits into hybrid ricedesignated HR180001 includes:

a) crossing a hybrid rice HR180001 plant, from which a representativesample of seed was deposited in the ATCC under the Budapest Treaty(Accession No. PTA-125519), with a plant of another rice cultivar thatcomprises a desired trait, to produce progeny plants, wherein thedesired trait(s) is selected from the group consisting of malesterility, herbicide resistance, insect resistance, modified fatty acidmetabolism, modified carbohydrate metabolism, and resistance tobacterial disease, fungal disease and viral disease;

b) selecting one or more progeny plants that have the desired trait(s)to produce selected progeny plants;

c) backcrossing the selected progeny plants with the HR180001 plants;

d) selecting for backcross progeny plants that have the desiredtrait(s); and

e) repeating steps (c) and (d) three or more times to produce selectedfourth or higher backcross progeny plants that comprise the desiredtrait(s).

A method of growing a blend of rice seed includes:

a) planting a blend comprising a first quantity of rice seed mixed witha second quantity of rice seed of another rice variety, rice hybrid orrice inbred;

b) growing the seeds to produce rice plants;

c) allowing cross pollination to occur between plants from firstquantity of seed and plants from second quantity of seed; and

d) harvesting seeds from the crossing the rice plants.

The blend may include seeds from a third, fourth or fifth rice variety,rice hybrid or rice inbred, and may include about 1% to about 95% ofhybrid rice HR180001 seeds.

A method of producing a blend of rice seeds, includes:

a) providing a first quantity of rice seed;

b) providing a second quantity of rice seed of another rice variety,rice inbred or rice hybrid; and

c) producing a blend comprised of mixing said first quantity of riceseed with said second quantity of rice seed.

The blend may include seeds from a third, fourth or fifth rice variety,and rice inbred, or rice hybrid and about 1% to about 95% of hybrid riceHR180001 seed.

DETAILED DESCRIPTION

Hybrid rice HR180001 is a very early maturing hybrid with a long grain,and low chalk values that was evaluated at multiple locations against abroad set of public varieties and potential hybrids for four years.

The hybrid disclosed herein has shown uniformity and stability asdescribed in the following hybrid rice description information. It hasbeen planted in a sufficient number of seasons with careful attention touniformity of plant type. The hybrid has been produced with continuedobservation for uniformity.

A representative sample of the hybrid rice seed HR180001 was depositedwith the ATCC (Accession No. PTA-125519) under the Budapest Treatyprovision.

The following embodiments and aspects thereof are described inconjunction with systems, tools and methods which are meant to beexemplary and illustrative, not limiting in scope.

Within the scope of the claims are hybrid rice seeds, designatedHR180001, the plants of hybrid rice HR180001, methods for producing arice plant produced by crossing hybrid rice HR180001 with itself oranother rice line or hybrid, and seeds and plants derived from thehybrid. “Derived” includes any plant part that traces its genetic originto the deposited seeds including hybrid plants, seeds, and any furtherprogeny or descendants of the hybrid derived by crossing hybrid riceHR180001 with other plants as a pollen donor or as a pollen recipient.Thus, any methods using hybrid rice HR180001 in backcrosses, hybridproduction, crosses to develop populations, and the like, are within thescope of the present disclosure. All plants which are a progeny of ordescend from hybrid rice HR180001 are within the scope of thisdisclosure. Hybrid rice HR180001 may be used in crosses with other,different, rice plants to produce first generation (F1) rice hybridseeds and plants with different, possibly superior characteristics.

Single gene or multiple gene converted plants of hybrid rice HR180001are disclosed. The single or multiple transferred gene(s) may preferablybe a dominant or recessive allele. The single or multiple transferredgene(s) will confer such traits as herbicide resistance, insectresistance, resistance to bacterial, fungal, or viral diseases, malefertility, male sterility, enhanced nutritional quality, and/orindustrial usage. The single or multiple gene(s) may be a naturallyoccurring rice gene, may be a gene modified as the result of artificialmutation of a naturally occurring gene, or a transgene introducedthrough genetic engineering techniques.

Regenerable cells are provided for use in tissue culture of hybrid riceHR180001. The tissue culture will preferably be capable of regeneratingplants having the physiological and morphological characteristics of theforegoing rice plant, and of regenerating plants having substantiallythe same genotype as the foregoing rice plant. Genetic variants ofhybrid rice HR180001 may be naturally generated through using tissueculture, or artificially induced utilizing mutagenic agents, or genomeediting techniques during tissue culture. Suitable regenerable cells insuch tissue cultures include embryos, protoplasts, meristematic cells,callus, pollen, cotyledon, leaves, flowers, anthers, roots, pistils,root tips, glumes, seeds, panicles or stems.

A blend consisting of rice seed of hybrid rice HR180001 with rice seedof a different inbred, rice variety, or rice hybrid is produced. Plantsare grown from said seed and cross pollination occurs between thedifferent plants produced from the seeds incorporated into the blend.The blend may also include a first quantity of seed of hybrid riceHR180001 with one, two, three, four, five or more quantities of riceseed of another rice hybrid, rice inbred or rice variety.

A blend of seed of hybrid rice HR180001 with seed of one, two, three,four, five or more of a different rice hybrid, rice variety or riceinbred is provided where hybrid rice HR180001 is present in proportionsfrom 1% up to 95% of the blend, is disclosed. Methods for planting theblend produced with seeds of hybrid rice HR180001 and seeds of one, twothree, four, five or more of another rice hybrid, rice variety or riceinbred and obtaining a crop with a mix of plants with hybrid riceHR180001 as a component. Further, harvest of seeds from a planted blendis for plants of which hybrid rice HR180001 is a component of the blend,for the purpose of utilizing such seeds for food; feed, as a rawmaterial in industry, or as a seed source for planting.

In addition to the exemplary aspects and embodiments describedpreviously, further aspects and embodiments will become apparent bystudy of the following descriptions.

TABLE 1 HYBRID RICE HR180001 DESCRIPTION Hybrid rice HR180001 has thefollowing morphologic and other characteristics, based primarily on datacollected in Alvin, TX.¹ Maturity Days to Flowering: 74 days fromemergence to 50% heading Maturity Class: Very early, (less than 75 days)Plant Height at Maturity Height: 116 cm Height Class: Tall (110 to 120cm) Culm Angle (Degrees from perpendicular after flowering): ErectInternode Color (after flowering): Green Strength (lodging resistance atmaturity): Strong Flag Leaf (After Heading) Length: 31.9 cm Width: 1.4cm Pubescence: Pubescent Leaf Angle: Erect Blade Color: Green Basal LeafSheath Color: Purple Ligule Length: 19.6 mm Color (late vegetativestate): Whitish Shape: Cleft, tip is split Collar Color (late vegetativestage): Light-green Auricle Color (late vegetative stage): Yellow-greenPanicle Length: 23.9 cm Type: Intermediate Secondary Branching: HeavyExertion (near maturity): Moderately well exerted (panicle base is abovethe collar of the flag leaf blade) Axis: Droopy Shattering: Low, (1-5%)Threshability: Intermediate (25-50% of grains removed) Grain (Spikelet)Awns (after full heading): absent Apiculus Color (at maturity): BrownStigma Color: Purple Stigma exertion (at flowering): 100% exertion,stigma fully outside glume Lemma and Palea Color (at maturity): StrawLemma and Palea Pubescence: Short hairs Spikelet Sterility (atmaturity): Fertile, 75-90% Grain (Seed) Paddy Measurements:  Length: 9.2mm  Width: 2.7 mm  L/W Ratio: 3.4  Thickness: 2.6 mm  Weight (1000grains): 24.9 g Brown Grain Measurements:  Length: 7.1 mm  Width: 2.2 mm L/W Ratio: 3.2  Thickness: 1.8 mm  Weight (1000 grains): 21.2 g MilledGrain Measurements:  Length: 6.6 mm  Width: 2.1 mm  L/W Ratio: 3.1 Thickness: 1.8 mm  Weight (1000 grains): 18.7 g Milling Yield (% wholekernel -head rice to rough rice): 60% Shape Class (length/width ratio):Long Seed Coat Color: Light brown Apparent Amylose: 20.5% AlkaliSpreading Value: 3 (2.3% KOH Solution) Gelatinization Temperature Type:high-intermediate Endosperm Type: Non-glutinous (non-waxy) EndospermTranslucency: Clear Endosperm Chalkiness: Small (less than 10% ofsample) Scent: Non-scented ¹Information was collected in Alvin, Texas,at a fertilization rate of 168 kg/ha N.

In the following tables, probability figures indicate the probabilityassociated with a paired Student's T-Test used to determine whether twosamples are likely to have come from the same two underlying populationsthat have the same mean. The N.S. notation means that there is nosignificant difference between the means of the two samples.

Hybrid rice HR180001 is a widely-adapted hybrid that can be grown in theUnited States (US). In Tables 2 and 3, data collected in the US andhybrid rice HR180001, is compared to Cheniere, a commonly grown cultivarin the US.

Description of Varieties Used for Comparison

Cheniere: an early, high yielding, high quality semi-dwarf long-grain.It has displayed excellent yield potential, good lodging resistance andmoderate resistance to physiological straight head. It is susceptible toblast and sheath blight. The variety has displayed excellent grainquality characteristics and is similar in maturity to Cypress. Saichuk,John et al., 2014 Rice Varieties and Management Tips. N.p.: LSU, 2014(U.S. Pat. No. 7,141,725, PTA-5613).

Table 2, column 2 shows the yield in kilograms per hectare, column 3shows the height in centimeters, column 4 shows the days to 50%flowering, column 5 shows the lodging score, column 6 gives the totalmilling percent, and column 7 shows the whole milling percent. Thenumber of observations over which the data was collected is shown in row4.

Table 2, hybrid rice HR180001 shows to be different from the US cultivarCheniere. The hybrid rice HR180001, unexpectedly, has significantlygreater grain yield, plant height, and lodging than the US cultivar,Cheniere. Yet, Cheniere has greater days to 50% flowering, and total andwhole milling percentages than hybrid rice HR180001. Data was collectedduring four years over a number of locations in the US.

TABLE 2 4 6 7 2 Plant Days to 5 Total Whole Yield Height 50% LodgingMilling Milling 1 1 (kg/ha) (cm) Flowering Score % % 2 HR180001 13,031110 79 5 72 59 3 Cheniere 9,742 98 85 2 73 66 4 Observations (n) 120 93114 120 123 123 5 Difference 3,289 12 −6 3 −1 −7 6 Probability 0.0000.000 0.000 0.007 0.000 0.000

In Table 3, column 2 shows the amylose percent, column 3 shows alkalispreading value (ASV), column 4 shows the milled grain length inmillimeters (Length), column 5 shows the milled grain width inmillimeters (Width), column 6 shows the milled grain length to widthratio (L/W Ratio), and column 7 shows the milled grain chalk percent.The number of observations over which the data was collected is shown inrow 4.

As shown in Table 3, the quality characteristics of the grain harvestedfrom hybrid rice HR180001 are different from those of cultivar Cheniere.Unexpectedly, hybrid rice HR180001 has a significantly higher milledgrain width and chalk percentage when compared to cultivar Cheniere.Cheniere has a higher amylose, ASV, and milled grain length to widthratio. Both hybrid rice HR180001 and Cheniere have similar milled grainlength values. Data was collected during four years over a number oflocations in the US.

TABLE 3 2 4 5 6 7 Amylose 3 Length Width L/W Chalk 1 1 % ASV (mm) (mm)Ratio % 2 HR180001 19 3.6 6.6 2.1 3.1 2 3 Cheniere 26 4.6 6.6 2.0 3.3 14 Observa- 64 64 122 122 122 98 tions (n) 5 Difference −7 −1.0 0 0.1−0.2 1 6 Probability 0.000 0.000 N.S. 0.000 0.000 0.000

In Tables 4 and 5, starch characteristics of hybrid rice HR180001 arecompared to Cheniere.

In Table 4, column 2 shows the peak viscosity expressed in RapidVisco-Analyzer units (RVU), column 3 shows the peak time in minutes,column 4 shows the trough in RVU, column 5 shows the trough time inminutes, column 6 shows the paste temperature in degrees Celsius, andcolumn 7 shows the paste time in minutes. In Table 5, column 2 shows thefinal viscosity in RVU, column 3 shows the breakdown in RVU, column 4shows the setback in RVU, column 5 shows the consistency of the starchin RVU, column 6 shows the whiteness, and column 7 shows thetransparency. The whiteness and transparency are expressed in lightreflectance and transparency units, respectively, as measured by theSatake Milling Degree Meter.

As shown in Tables 4 and 5, hybrid rice HR180001 has a higher peakviscosity, peak time, trough, trough time, final viscosity, breakdown,consistency, and whiteness when compared to rice variety Cheniere.However, hybrid rice HR180001 has lower paste temperature, paste time,set back, and transparency when compared to rice variety Cheniere. Datapresented in Tables 4 and 5 is from analysis made at the RiceTec, Inc.Grain Quality Lab with grain harvested in Alvin, Tex.

TABLE 4 2 6 7 Peak 3 5 Paste Paste Viscos- Peak 4 Trough Temper- Timeity Time Trough Time ature (min- 1 1 (RVU) (minutes) (RVU) (minutes) (°C.) utes) 2 HR180001 258.6 5.7 132.1 8.3 84.3 3.9 3 Cheniere 130.5 5.675.6 8.0 89.9 4.4 4 Difference 128.1 0.1 56.5 0.3 −5.6 −0.5

TABLE 5 2 6 Final 3 4 5 Whiteness Viscos- Break Set Consis- (light 7 ityDown back tency reflec- Trans- 1 1 (RVU) (RVU) (RVU) (RVU) tance)parency 2 HR180001 247.4 126.6 −11.2 115.4 49.8 2.7 3 Cheniere 187.654.9 57.1 111.9 47.4 3.1 4 Difference 59.8 71.7 −68.3 3.5 2.4 −0.4

Definitions

Unless otherwise defined, all technical and scientific terms herein havethe same meaning as commonly understood by one of ordinary skill in theart to which this disclosure belongs. The terminologies that are used inthe description of HR180001 herein are for the purpose of describingparticular embodiments only and not intended to the limiting. Allpublications, patent applications, patent, and other referencesmentioned herein are incorporated by reference in their entirety. In thedescription and tables herein, a number of terms are used. In order toprovide a clear and consistent understanding of the specification andclaims, including the scope to be given such terms, the followingdefinitions are provided:

Alkali Spreading Value (ASV). A 1-7 index used as predictor of starchgelatinization temperature and established by the extent ofdisintegration of milled rice kernel in contact with a dilute alkalisolution. Standard long grains have a 3 to 5 Alkali Spreading Value.

Allele. Allele is any one of many alternative forms of a gene, all ofwhich usually relate to one trait or characteristic. In a diploid cellor organism, the two alleles of a given gene occupy corresponding locion a pair of homologous chromosomes.

Alter. The utilization of up-regulation, down-regulation, or genesilencing.

Amylose. Type of grain starch that affects cooking behaviour. As suchits measured quantity in rice is used to establish cooking properties ofStandard US grain classes, or types (long, medium and short-grain).

Apiculus. Structures on the tip of the glume which are protrusions ofthe middle nerves of the bracts of the lemma and palea.

Apparent Amylose Percent. The percentage of the endosperm starch ofmilled rice that is amylose. Standard long grains contain 20 to 23percent amylose. Rexmont-type long grains contain 24 to 25 percentamylose. Short and medium grains contain 14 to 16 percent amylose. Waxyrice contains zero percent amylose. Amylose values, like mostcharacteristics of rice, will vary over environments. “Apparent” refersto the procedure for determining amylose, which may also involvemeasuring some long chain amylopectin molecules that bind to some of theamylose molecules. These amylopectin molecules actually act similar toamylose in determining the relative hard or soft cookingcharacteristics.

Auricle. Paired small appendages on either side of the base of the leafblade.

Awns. An extension of the lemma apiculus.

Backcrossing. Process of crossing a hybrid progeny to one of theparents, for example, a first-generation hybrid F1 with one of theparental genotypes of the F1 hybrid.

Basal Leaf Sheath. Portion of the leaf that envelops the culm above thelowest node.

Breakdown. The Peak Viscosity minus the Trough Viscosity.

Cell. Cell as used herein includes a plant cell, whether isolated, intissue culture or incorporated in a plant or plant part.

Chalk. An opaque region of the rice kernel resulting from loose packingof the starch granules. Chalk may occur throughout or in a part of thekernel.

Collar. Where the leaf sheath and leaf blade join

Consistency. The Final Viscosity minus the Trough Viscosity.

Cotyledon. A cotyledon is a type of seed leaf. The cotyledon containsthe food storage tissues of the seed.

Culm. The rice plant's stem.

Cultivar. Cultivated variety, which is a genotype under cultivation.

Days to 50% flowering. Number of days from emergence to the day when 50%of all panicles are exerted at least partially through the leaf sheath.A measure of growth duration.

Embryo. The embryo is the small plant contained within a mature seed.

Endosperm. The largest part of the grain usually referred to as milledor white rice, having the seed coat (bran) and embryo (germ) removed.

Essentially all the physiological and morphological characteristics. Aplant having essentially all the physiological and morphologicalcharacteristics of the hybrid or cultivar, except for the newcharacteristics derived from the converted gene.

Final Viscosity. The stickiness of rice flour/water slurry after beingheated to 95° C. and uniformly cooled to 50° C. in a standardizedinstrument, specifically the Rapid Visco Analyzer. Viscosity at the endof the test also defined as Cool Paste Viscosity. (AACC Method 61-02)

Grain Length (L). Length of a whole rice grain measured in millimeters.

Gelatinization Temperature. The temperature at which the consistency ofa rice flour-water mixture changes into a jelly. Correlates with thecooking time and texture of a rice product.

Gene Silencing. The interruption or suppression of the expression of agene at the level of transcription or translation.

Genetically Modified. Describes an organism that has received geneticmaterial from another, or had its genetic material modified, resultingin a change in one or more of its phenotypic characteristics. Methodsused to modify, introduce or delete the genetic material may includemutation breeding, genome editing, backcross conversion, genetictransformation, single and multiple gene conversion, and/or direct genetransfer.

Genome Editing. A type of genetic engineering in which DNA is inserted,replaced, modified or removed from a genome using artificiallyengineered nucleases or other targeted changes using homologousrecombination.

Genotype. Refers to the genetic constitution of a cell or organism.

Grain Width (W). Width of a whole rice grain measured in millimeters.

Grain Yield. Weight of grain harvested from a given area. Grain yieldcould also be determined indirectly by multiplying the number ofpanicles per area, by the number of grains per panicle, and by grainweight.

Harvest Moisture. The percent of moisture of the grain when harvested.

Hybrid. A plant that has been bred from two different parent plants.

Inbred Line. Seed and subsequent crops will have the same genetic makeupas the parent crop.

Internode. Area between nodes that is hollow with smooth outer surfacesand varying lengths.

Lemma and Palea. Together known as the glume, the larger five-nervedbract (lemma) that partly envelops the smaller three-nerved bract(palea), contain the floral organs.

Length/Width (L/W) Ratio. This ratio is determined by dividing theaverage length (L) by the average width (W).

Ligule. A membranous structure on the inner junction where the leafsheath and the leaf blade meet that can vary in size, shape and color.

Linkage. Refers to a phenomenon wherein alleles on the same chromosometend to segregate together more often than expected by chance if theirtransmission was independent.

Linkage Disequilibrium. Refers to a phenomenon wherein alleles tend toremain together in linkage groups when segregating from parents tooffspring, with a greater frequency than expected from their individualfrequencies.

Locus. A locus is a position, on a chromosome that confers one or moretraits such as, for example, male sterility, herbicide resistance,insect resistance, disease resistance, waxy starch, modified fatty acidmetabolism, modified phytic acid metabolism, modified carbohydratemetabolism and modified protein metabolism. The trait may be, forexample, conferred by a naturally occurring gene introduced into thegenome of the variety by backcrossing, a natural or induced mutation, ora transgene introduced through genetic transformation techniques. Alocus may comprise one or more alleles integrated at a singlechromosomal location.

Lodging Percent. Lodging is a subjective measured rating, and is thepercentage of plant stems leaning or fallen completely to the groundbefore harvest.

Milled grain length. The length of the rice grain after the hull andpericarp are removed.

Milled grain width. The width of the rice grain after the hull andpericarp are removed.

Mixing. Physically mixing whole seeds of two or more genotypes of riceseed. For example, one of the genotypes of rice seed is hybrid riceHR180001 mixed with more than one, two, three, four, five or moregenotypes of rice seed.

Multiple Gene Converted (Conversion). Multiple gene converted(conversion) includes plants developed by a plant breeding techniquecalled backcrossing, wherein essentially all of the desiredmorphological and physiological characteristics of an inbred arerecovered, while retaining two or more genes transferred into the inbredvia crossing and backcrossing. The term can also refer to theintroduction of multiple genes through genetic engineering techniquesknown in the art.

1000 Grain Weight. The weight of 1000 rice grains as measured in grams.

Paste Temperature. The temperature at which a defined flour-watermixture exhibits an initial viscosity increase under a standardizedprotocol utilizing the Rapid Visco Analyzer. Paste Temperature is anindication of gelatinization temperature.

Paste Time. The time at which Paste Temperature occurs.

Peak Temperature. The temperature at which Peak Viscosity is attained.

Peak Time. The time at which Peak Viscosity is attained.

Peak Viscosity. The maximum viscosity attained during heating when astandardized protocol utilizing the Rapid Visco Analyzer is applied to adefined rice flour-water slurry. (AACC Method 61-02).

Percent Identity. The extent to which two sequences have the sameresidues at the same positions in an alignment. Percent identity, asused herein, refers to the comparison of the homozygous alleles of tworice varieties. Percent identity is determined by comparing astatistically significant number of the homozygous alleles of twodeveloped varieties. For example, a percent identity of 90% between ricevariety 1 and rice variety 2 means that the two varieties have the sameallele at 90% of their loci.

Percent Similarity. The extent to which nucleotide or protein sequencesare related can be expressed as percent identity. Percent similarity, asused herein, refers to the comparison of the homozygous alleles of arice variety with another rice plant, and if the homozygous allele ofboth rice plants matches at least one of the alleles from the otherplant then they are scored as similar. Percent similarity is determinedby comparing a statistically significant number of loci and recordingthe number of loci with similar alleles as a percentage. A percentsimilarity of 90% between the rice plant of this invention and anotherplant means that the rice plant matches at least one of the alleles ofthe other rice plant at 90% of the loci.

Plant. As used herein, the term “plant” includes reference to animmature or mature whole plant, including a plant from which seed orgrain or anthers have been removed. Seed or embryo that will produce theplant is also considered to be the plant.

Plant Height. Plant height in centimeters is taken from soil surface tothe tip of the extended panicle at harvest.

Plant Part. As used herein, the term “plant part” (or a rice plant, or apart thereof) includes protoplasts, leaves, stems, roots, root tips,anthers, seed, grain, embryo, pollen, ovules, cotyledon, hypocotyl,glumes, panicles, flower, shoot, tissue, cells, meristematic cells andthe like.

Pubescence. This refers to a covering of very fine hairs closelyarranged on the leaves, stems and glumes of the rice plant.

Quantitative Trait Loci (QTL). Genetic loci that controls to some degreenumerically measurable traits that are usually continuously distributed.

Regeneration. Regeneration refers to the development of a plant fromtissue culture.

Resistance/Resistant². The inherited ability of a plant to survive andreproduce following exposure to a dose of herbicide normally lethal tothe wild type; resistance may be naturally occurring or induced by suchtechniques as genetic engineering or selection of variants produced bytissue culture or mutagenesis. ²Weed Science Society of America, WeedTechnology, vol. 12, issue 4 (October-December, 1998, p. 789)

RVA. Rapid Visco Analyzer is a widely used laboratory instrumentutilized to examine the cooking properties of rice flour (i.e. pastetime and thickening ability).

RVU. RAPID VISCO UNITS refer to the measurement units of the RVA.

Satake Milling Degree meter. A milling meter that simultaneouslymeasures the degree of milling, comparative whiteness and degree oftransparency of milled rice samples.

Semi-dwarf. A variety that is smaller than normal for its species.

Setback. The Final Viscosity minus Peak Viscosity.

Single Gene Converted (Conversion). Single gene converted (conversion)includes plants developed by a plant breeding technique calledbackcrossing wherein essentially all of the desired morphological andphysiological characteristics of an inbred are recovered, whileretaining a single gene transferred into the inbred via crossing andbackcrossing. The term can also refer to the introduction of a singlegene through genetic engineering techniques known in the art.

Tillering. New culms arising from buds in the axil.

Tolerance/Tolerant². Resistance/tolerance are used somewhatinterchangeably herein; for a specific rice plant genotype informationis provided on the herbicide applied, the strength of the herbicide, andthe response of the plant.

Total Milling (also called Milling Yield). The quantity of total milledrice produced in the milling of rough rice to a well-milled degree; itis usually expressed as a percent of rough rice by weight, but whenspecified, may be expressed as a percent of brown rice.

Transgene. A segment of DNA containing a gene sequence that has beenisolated from one organism and is introduced into a different organism.

Transparency. The percentage of light transmitted through a milled grainof standard depth.

Trough Time. The time at which Trough Viscosity is attained.

Trough Viscosity. The minimum viscosity that occurs after Peak viscositywhen a standardized protocol utilizing the Rapid Visco Analyzer isapplied to a defined rice flour-water slurry. (AACC Method 61-02)

Variety. A group of plants having distinct uniform and stable traitswhich has been recommended for cultivation.

Whiteness. The percentage of light reflected from the milled grainsample.

Whole Milling (also called Head Rice Milling Yield). The quantity ofmilled head (¾ to whole kernels) rice produced in the milling of roughrice to a well-milled degree, usually expressed in the United States asa percent of rough rice by weight.

The use of the terms “a,” “an,” and “the,” and similar referents in thecontext of describing the invention (especially in the context of thefollowing claims) are to be construed to cover both the singular and theplural, unless otherwise indicated herein or clearly contradicted bycontext. The terms “comprising,” “having,” “including,” and “containing”are to be construed as open-ended terms (i.e., meaning “including, butnot limited to,”) unless otherwise noted. Recitation of ranges of valuesherein are merely intended to serve as a shorthand method of referringindividually to each separate value falling within the range, unlessotherwise indicated herein, and each separate value is incorporated intothe specification as if it were individually recited herein. Forexample, if the range 10-15 is disclosed, then 11, 12, 13, and 14 arealso disclosed. All methods described herein can be performed in anysuitable order unless otherwise indicated herein or otherwise clearlycontradicted by context. The use of any and all examples, or exemplarylanguage (e.g., “such as”) provided herein, is intended merely to betterilluminate the invention and does not pose a limitation on the scope ofthe invention unless otherwise claimed. No language in the specificationshould be construed as indicating any non-claimed element as essentialto the practice of the invention.

Materials and Methods

Methods for producing a rice plant include crossing a first parent riceplant with a second parent rice plant, wherein the first or second riceplant is a rice plant from hybrid rice HR180001. Further, both first andsecond parent rice plants may be from the hybrid rice HR180001.Therefore, other methods of using hybrid rice HR180001 include: selfing,backcrosses, hybrid breeding, and crosses to populations. Any plantsproduced using hybrid rice HR180001 as a parent is within the scope ofthis invention.

Methods for producing a hybrid rice HR180001-derived rice plant bycrossing hybrid rice HR180001 with a second rice plant and growing theprogeny seed, and repeating the crossing and growing steps with hybridrice HR180001-derived plant from 0 to 7 times is disclosed. Any suchmethods using the hybrid rice HR180001 are disclosed, including:selfing, backcrosses, hybrid production, crosses to populations, and thelike. All plants produced using hybrid rice HR180001 as a parent arewithin the scope of these claims, including plants derived from hybridrice HR180001.

It should be understood that hybrid rice HR180001 can, through routinemanipulation of cytoplasm or other factors, be produced in amale-sterile form. Such embodiments are also contemplated within thescope of the present claims.

As used herein, the term plant includes plant cells, plant protoplasts,plant cell tissue cultures from which rice plants can be regenerated,plant calli, plant clumps and plant cells that are intact in plants orparts of plants, such as embryos, pollen, ovules, flowers, glumes,panicles, leaves, stems, roots, root tips, anthers, pistils and thelike.

Methods of Introducing New Trait or Locus into Hybrid Rice HR180001

Hybrid rice HR180001 represents a new base genetic hybrid into which anew locus, loci or trait(s) may be introgressed. Rice transformation,gene editing, backcross conversion with single or multiple genes, tissueculture method, double haploid techniques, pedigree breeding, mutationbreeding and backcrossing are important methods that can be used toaccomplish such an introgression.

A. Rice Transformation

The advent of new molecular biological techniques has allowed theisolation and characterization of genetic elements with specificfunctions such as encoding specific protein products. Scientists in thefield of plant biology developed a strong interest in engineering thegenome of plants to contain and express foreign genetic elements, oradditional, or modified versions of native or endogenous in order toalter the traits of a plant in a specific manner. Any DNA sequenceswhether from a different species or from the same species which areinserted into the genome via transformation are referred to hereincollectively as “transgenes”. In some embodiments, a transgenic variantof hybrid rice HR180001 may contain at least one transgene, but couldcontain multiple transgenes. Over the last fifteen to twenty years,several methods for producing transgenic plants have been developed andrelate to transformed versions of the parents of the claimed hybrid.

A process for producing hybrid rice HR180001 with a desired trait,includes transforming hybrid rice HR180001 with a transgene that confersthe desired trait. Another embodiment is the product produced by thisprocess. The desired trait may be one or more of herbicide resistance,insect resistance, disease resistance, decreased phytate, or modifiedfatty acid or carbohydrate metabolism. The specific gene may be anyknown in the art or listed herein, including; a polynucleotideconferring resistance to imidazolinone, sulfonylurea, glyphosate,glufosinate, triazine, benzonitrile, cyclohexanedione, phenoxyproprionic acid, isoxazole, triketone and L-phosphinothricin; apolynucleotide encoding a Bacillus thuringiensis polypeptide, apolynucleotide encoding phytase, FAD-2, FAD-3, galactinol synthase or araffinose synthetic enzyme.

Numerous methods for plant transformation have been developed, includingbiological and physical plant transformation protocols. See, forexample, Miki et al., “Procedures for Introducing Foreign DNA intoPlants” in Methods in Plant Molecular Biology and Biotechnology, GlickB. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages67-88.

1. Agrobacterium-mediated Transformation—One method of ricetransformation is based on the natural transformation system ofAgrobacterium. See, for example, Horsch et al., Science 227:1229 (1985).A. tumefaciens and A. rhizogenes are plant pathogenic soil bacteriawhich genetically transform plant cells. The Ti and Ri plasmids of A.tumefaciens and A. rhizogenes, respectively, carry genes responsible forgenetic transformation of the plant. See, for example, Kado, C. I.,Crit. Rev. Plant Sci. 10:1 (1991). Descriptions of Agrobacterium vectorsystems and methods for Agrobacterium-mediated gene transfer areprovided by Gruber et al., supra, Miki et al., supra, and Moloney etal., Plant Cell Reports 8:238 (1989). See also, U.S. Pat. No. 5,591,616issued Jan. 7, 1997.

2. Direct Gene Transfer—Despite the fact the host range forAgrobacterium-mediated transformation is broad, some major cereal cropspecies and gymnosperms have generally been recalcitrant to this mode ofgene transfer, even though some success has recently been achieved inrice and corn. Hiei et al., The Plant Journal 6:271-282 (1994) and U.S.Pat. No. 5,591,616 issued Jan. 7, 1997. Several methods of planttransformation collectively referred to as direct gene transfer havebeen developed as an alternative to Agrobacterium-mediatedtransformation.

A generally applicable method of plant transformation ismicroprojectile-mediated transformation wherein DNA is carried on thesurface of microprojectiles measuring 1 to 4 μm. The expression vectoris introduced into plant tissues with a biolistic device thataccelerates the microprojectiles to speeds of 300 to 600 m/s which issufficient to penetrate plant cell walls and membranes. Sanford et al.,Part. Sci. Technol. 5:27 (1987), Sanford, J. C., Trends Biotech. 6:299(1988), Klein et al., Bio/Technology 6:559-563 (1988), Sanford, J. C.,Physiol Plant 7:206 (1990), Klein et al., Biotechnology 10:268 (1992).In corn, several target tissues can be bombarded with DNA-coatedmicroprojectiles in order to produce transgenic plants, including, forexample, callus (Type I or Type II), immature embryos, and meristematictissue.

Another method for physical delivery of DNA to plants is sonication oftarget cells. Zhang et al., Bio/Technology 9:996 (1991). Additionally,liposome and spheroplast fusion have been used to introduce expressionvectors into plants. Deshayes et al., EMBO J., 4:2731 (1985), Christouet al., Proc Natl. Acad. Sci. U.S.A. 84:3962 (1987). Direct uptakes ofDNA into protoplasts using CaCl2 precipitation, polyvinyl alcohol orpoly-L-ornithine have also been reported. Hain et al., Mol. Gen. Genet.199:161 (1985) and Draper et al., Plant Cell Physiol. 23:451 (1982).Electroporation of protoplasts, whole cells, and tissues have also beendescribed. Donn et al., In Abstracts of VIIth International Congress onPlant Cell and Tissue Culture IAPTC, A2-38, p 53 (1990); D'Halluin etal., Plant Cell 4:1495-1505 (1992) and Spencer et al., Plant Mol. Biol.24:51-61 (1994).

Following transformation of rice target tissues, expression ofselectable marker genes that are described, allows for preferentialselection of transformed cells, tissues and/or plants, usingregeneration and selection methods now well known in the art.

B. Gene Editing Technique

In general, methods to modify, edit or alter plant endogenous genomicDNA include altering the plant native DNA sequence or a pre-existingsequence including regulatory elements, coding and non-coding sequences.These methods can be used, for example, to target nucleic acids topre-engineered target recognition sequences in the genome. Suchpre-engineered target sequences may be introduced by genome editing ormodification. As an example, a genetically modified plant variety isgenerated using “custom” or engineered endonucleases such asmeganucleases produced to modify plant genomes (see e.g., WO2009/114321; Gao et al. (2010) Plant Journal 1:176-187). Anothersite-directed engineering method is through the use of zinc fingerdomain recognition coupled with the restriction properties ofrestriction enzyme. See e.g., Umov, et al., (2010) Nat Rev Genet.11(9):636-46; Shukla, et al., (2009) Nature 459 (7245):437-41. Atran-scription activator-like (TAL) effector-DNA modifying enzyme (TALEor TALEN) is also used to engineer changes in plant genome. See e.g.,US20110145940, Cermak et al. (2011), Nucleic Acids Res. 39(12) and Bochet al., (2009), Science 326(5959): 1509-12. Site-specific modificationof plant genomes can also be performed using the bacterial type IICRISPR (clustered regularly interspaced short pal-indromic repeats)/Cas(CRISPR-associated) system. See e.g., Belhaj et al., (2013), PlantMethods 9: 39. The Cas9/guide RNA-based system allows targeted cleavageof genomic DNA guided by a customizable small noncoding RNA in plants(see e.g., WO 2015026883A1, incorporated herein by reference).

C. Backcross Conversions

A backcross conversion of hybrid rice HR180001 occurs when DNA sequencesare introduced through backcrossing (Hallauer et al, 1988, “CornBreeding” Corn and Corn Improvements, No. 18, pp. 463-481), with hybridrice HR180001 utilized as the recurrent parent. Both naturally occurringand transgenic DNA sequences may be introduced through backcrossingtechniques. A backcross conversion may produce a plant with a trait(s),locus or loci conversion in at least two or more backcrosses, includingat least 2 crosses, at least 3 crosses, at least 4 crosses, at least 5crosses and the like. Molecular marker assisted breeding or selectionmay be utilized to reduce the number of backcrosses necessary to achievethe backcross conversion. For example, see Openshaw, S. J. et al.,Marker-assisted Selection in Backcross Breeding. In: ProceedingsSymposium of the Analysis of Molecular Data, August 1994, Crop ScienceSociety of America, Corvallis, Oreg., where it is demonstrated that abackcross conversion can be made in as few as two backcrosses.

The complexity of the backcross conversion method depends on the type oftrait being transferred (single genes or closely linked genes vs.unlinked genes), the level of expression of the trait, the type ofinheritance (cytoplasmic or nuclear) and the types of parents includedin the cross. It is understood by those of ordinary skill in the artthat for single gene traits that are relatively easy to classify, thebackcross method is effective and relatively easy to manage. (SeeHallauer et al. in Corn and Corn Improvement, Sprague and Dudley, ThirdEd. 1998). Desired traits that may be transferred through backcrossconversion include, but are not limited to, sterility (nuclear andcytoplasmic), fertility restoration, nutritional enhancements, droughttolerance, nitrogen utilization, altered fatty acid profile, lowphytate, industrial enhancements, disease resistance (bacterial, fungalor viral), insect resistance and herbicide resistance. In addition, anintrogression site itself, such as an FRT site, Lox site or othersite-specific integration site, may be inserted by backcrossing andutilized for direct insertion of one or more genes of interest into aspecific plant variety. In some embodiments, the number of loci that maybe backcrossed into hybrid rice HR180001 is at least one, but could bemultiple loci. A single locus may contain several transgenes, such as atransgene for disease resistance that, in the same expression vector,also contains a transgene for herbicide resistance. The gene forherbicide resistance may be used as a selectable marker and/or as aphenotypic trait. A single locus conversion of a site-specificintegration system allows for the integration of multiple genes at theconverted loci.

D. Tissue Culture and In-Vitro Regeneration of Rice Plants

Further reproduction of the hybrid can occur by tissue culture andregeneration. Tissue culture of various tissues of rice and regenerationof plants therefrom is well known and widely published. For example,reference may be had to Komatsuda, T. et al., Crop Sci. 31:333-337(1991); Stephens, P. A., et al., Theor. Appl. Genet. (1991) 82:633-635;Komatsuda, T. et al., Plant Cell, Tissue and Organ Culture, 28:103-113(1992); Dhir, S. et al., Plant Cell Reports (1992) 11:285-289; Pandey,P. et al., Japan J. Breed. 42:1-5 (1992); and Shetty, K., et al., PlantScience 81:245-251 (1992); as well as U.S. Pat. No. 5,024,944 issuedJun. 18, 1991 to Collins et al., and U.S. Pat. No. 5,008,200 issued Apr.16, 1991 to Ranch et al. Thus, another aspect of this invention is toprovide cells which upon growth and differentiation produce rice plantshaving the physiological and morphological characteristics of hybridrice HR180001.

As used herein, the term “tissue culture” indicates a compositioncomprising isolated cells of the same or a different type or acollection of such cells organized into parts of a plant. Exemplarytypes of tissue are protoplasts, calli, plant clumps, and plant cellsthat can generate tissue culture that are intact in plants or parts ofplants, such as embryos, pollen, flowers, seeds, glumes, panicles,leaves, stems, roots, root tips, anthers, and the like. Means forpreparing and maintaining plant tissue culture are well known in theart. By way of example, a tissue culture comprising organs has been usedto produce regenerated plants. U.S. Pat. Nos. 5,959,185; 5,973,234 and5,977,445 describe certain techniques, the disclosures of which areincorporated herein by reference.

As used herein, the term “plant” includes plant cells, plantprotoplasts, plant cells of tissue culture from which rice plants can beregenerated, plant calli, plant clumps, and plant cells that are intactin plants or parts of plants, such as pollen, flowers, embryos, ovules,seeds, panicles, glumes, leaves, stems, pistils, anthers and the like.Thus, another aspect of this invention is to provide for cells whichupon growth and differentiation produce a cultivar having essentiallyall of the physiological and morphological characteristics of hybridrice HR180001. Genetic variants of hybrid rice HR180001 can also beobtained as a result of the tissue culture process. Variants recoveredby tissue culture of hybrid rice HR180001 are another aspect of thisdisclosure.

A rice plant may be regenerated from a tissue culture of the hybrid riceplant disclosed herein. As is well known in the art, tissue culture ofrice can be used for the in vitro regeneration of a rice plant. Tissueculture of various tissues of rice and regeneration of plants therefromis well known and widely published. For example, reference may be had toChu, Q. R., et al., (1999) “Use of bridging parents with high antherculturability to improve plant regeneration and breeding value in rice”,Rice Biotechnology Quarterly 38:25-26; Chu, Q. R., et al., (1998), “Anovel plant regeneration medium for rice anther culture of Southern U.S.crosses”, Rice Biotechnology Quarterly 35:15-16; Chu, Q. R., et al.,(1997), “A novel basal medium for embryogenic callus induction ofSouthern US crosses”, Rice Biotechnology Quarterly 32:19-20; and Oono,K., “Broadening the Genetic Variability By Tissue Culture Methods”, Jap.J. Breed. 33 (Supp1.2), 306-307, illus. 1983. Thus, another aspect ofthis invention is to provide cells which upon growth and differentiationproduce rice plants having the physiological and morphologicalcharacteristics of hybrid rice HR180001.

Duncan, et al., Planta 165:322-332 (1985), reflects that 97% of theplants cultured that produced callus were capable of plant regeneration.Subsequent experiments with both cultivars and hybrids produced 91%regenerable callus that produced plants. In a further study in 1988,Songstad, et al., Plant Cell Reports 7:262-265 (1988), reports severalmedia additions that enhance regenerability of callus of two cultivars.Other published reports also indicated that “non-traditional” tissuesare capable of producing somatic embryogenesis and plant regeneration.K. P. Rao et al., Maize Genetics Cooperation Newsletter, 60:64-65(1986), refers to somatic embryogenesis from glume callus cultures andB. V. Conger, et al., Plant Cell Reports, 6:345-347 (1987) indicatessomatic embryogenesis from the tissue cultures of corn leaf segments.Thus, it is clear from the literature that the state of the art is suchthat these methods of obtaining plants are routinely used and have avery high rate of success.

E. Production of Double Haploids

The production of double haploids can also be used for the developmentof plants with a homozygous phenotype in the breeding program. Forexample, a rice plant for which hybrid rice HR180001 is a parent can beused to produce double haploid plants. Double haploids are produced bythe doubling of a set of chromosomes (1 N) from a heterozygous plant toproduce a completely homozygous individual. For example, see Wan et al.,“Efficient Production of Doubled Haploid Plants Through ColchicineTreatment of Anther-Derived Maize Callus”, Theoretical and AppliedGenetics, 77:889-892, 1989 and U.S. Pat. No. 7,135,615.

Methods for obtaining haploid plants are also disclosed in Kobayashi, M.et al., Journ. of Heredity 71(1):9-14, 1980, Pollacsek, M., Agronomie(Paris) 12(3):247-251, 1992; Cho-Un-Haing et al., Journ. of Plant Biol.,1996, 39(3):185-188; Verdoodt, L., et al., February 1998, 96(2):294-300;Genetic Manipulation in Plant Breeding, Proceedings InternationalSymposium Organized by EUCARPIA, Sep. 8-13, 1985, Berlin, Germany;Thomas, W J K, et al. (2003) “Doubled haploids in breeding” in DoubledHaploid Production in Crop Plants. Maluszynski, M., et al. (Eds.)Dordrecht, the Netherland Kluwer Academic Publishers. pp. 337-349.

F. Pedigree Breeding

Pedigree breeding starts with the crossing of two genotypes, such ashybrid rice HR180001 and another rice plant having one or more desirablecharacteristics that is lacking or which complements hybrid riceHR180001. Descriptions of breeding methods that are commonly used fordifferent traits and crops can be found in one of several referencebooks (e.g., Allard, 1960; Simmonds, 1979; Sneep et al., 1979; Fehr,1987). If the two original parents do not provide all the desiredcharacteristics, other sources can be included in the breedingpopulation. In the pedigree method, superior plants are selfed andselected in successive filial generations. In the succeeding filialgenerations, the heterozygous condition gives way to homogeneousvarieties as a result of self-pollination and selection. Typically, inthe pedigree method of breeding, five or more successive filialgenerations of selfing and selection is practiced: F1 to F2; F2 to F3;F3 to F4; F4 to F5, etc. After a sufficient amount of inbreeding,successive filial generations will serve to increase seed of thedeveloped variety. Preferably, the developed variety compriseshomozygous alleles at about 95% or more of its loci.

In addition to being used to create a backcross conversion, backcrossingcan also be used in combination with pedigree breeding. As discussedpreviously, backcrossing can be used to transfer one or morespecifically desirable traits from one variety, the donor parent, to adeveloped variety called the recurrent parent, which has overall goodagronomic characteristics yet lacks that desirable trait or traits.However, the same procedure can be used to move the progeny toward thegenotype of the recurrent parent but at the same time retain manycomponents of the non-recurrent parent by stopping the backcrossing atan early stage and proceeding with selfing and selection. For example, arice variety may be crossed with another rice variety to produce afirst-generation progeny plant. The first-generation progeny plant maythen be backcrossed to one of its parent varieties to create a BC1 orBC2. Progeny are selfed and selected so that the newly developed varietyhas many of the attributes of the recurrent parent and yet several ofthe desired attributes of the non-recurrent parent. This approachleverages the value and strengths of the recurrent parent for use in newrice varieties.

Therefore, an embodiment within the scope of the claims is a method ofmaking a backcross conversion of hybrid rice HR180001, comprising thesteps of crossing a plant of hybrid rice HR180001 with a donor plantcomprising a desired trait, selecting an F1 progeny plant comprising thedesired trait, and backcrossing the selected F1 progeny plant to a plantof hybrid rice HR180001. This method may further comprise the step ofobtaining a molecular marker profile of hybrid rice HR180001 and usingthe molecular marker profile to select for a progeny plant with thedesired trait and the molecular marker profile of hybrid rice HR180001.In one embodiment the desired trait is a mutant gene or transgenepresent in the donor parent.

G. Mutation Breeding

Mutation breeding is another method of introducing new traits intohybrid rice HR180001. Mutations that occur spontaneously or areartificially induced can be useful sources of variability for a plantbreeder. The goal of artificial mutagenesis is to increase the rate ofmutation for a desired characteristic. Mutation rates can be increasedby many different means including temperature, long-term seed storage,tissue culture conditions, radiation; such as X-rays, Gamma rays (e.g.cobalt 60 or cesium 137), neutrons, (product of nuclear fission byuranium 235 in an atomic reactor), Beta radiation (emitted fromradioisotopes such as phosphorus 32 or carbon 14), or ultravioletradiation (preferably from 2500 to 2900 nm), or chemical mutagens suchas base analogues, (5-bromo-uracil), related compounds (8-ethoxycaffeine), antibiotics (streptonigrin), alkylating agents (sulfurmustards, nitrogen mustards, epoxides, ethylenamines, sulfates,sulfonates, sulfones, lactones), azide, hydroxylamine, nitrous acid, oracridines. Once a desired trait is observed through mutagenesis thetrait may then be incorporated into existing germplasm by traditionalbreeding techniques. Details of mutation breeding can be found in“Principles of Cultivar Development” Fehr, 1993 Macmillan PublishingCompany. In addition, mutations created in other rice plants may be usedto produce a backcross conversion of hybrid rice HR180001 that comprisessuch mutation.

H. Breeding with Molecular Markers

Molecular markers may be used in plant breeding methods utilizing hybridrice HR180001. Isozyme Electrophoresis and RFLPs have been widely usedto determine genetic composition. See for example, Dinka, S. J., et al.(2007) “Predicting the size of the progeny mapping population requiredto positionally clone a gene” Genetics. 176(4):2035-54; Gonzalez, C., etal. (2007) “Molecular and pathogenic characterization of new Xanthomonasoryzae strains from West Africa” Mol. Plant Microbe Interact.20(5):534-546; Jin, H., et al. (2006) “Molecular and cytogeniccharacterization of an Oryza officinalis-O. sativa chromosome 4 additionhybrid and its progenies” Plant Mol. Biol. 62(4-5):769-777; Pan, G., etal. (2006) “Map-based cloning of a novel rice cytochrome P450 geneCYP81A6 that confers resistance to two different classes of herbicides”Plant Mol. Biol. 61(6):933-943.; Huang, W., et al. (2007) “RFLP analysisfor mitochondrial genome of CMS-rice” Journal of Genetics and Genomics.33(4):330-338; Yan, C. J., et al. (2007) “Identification andcharacterization of a major QTL responsible for erect panicle trait injaponica rice (Oryza sativa L.)” Theor. Appl. Genetics.DOI:10.1007/s00122-007-0635-9; and I. K. Vasil (ed.) DNA-based markersin plants. Kluwer Academic Press Dordrecht, the Netherlands.

SNP technology is currently the most efficient and practical markertechnology; more marker loci can be routinely used. Gealy, David, et al.(2005) “Insights into the Parentage of Rice/red Rice Crosses Using SSRAnalysis of US Rice Cultivars and Red Rice Populations”. Rice TechnicalWorking Group Meeting Proceedings. Abstract p. 179.; Lawson, Mark J., etal. (2006) “Distinct Patterns of SSR Distribution in the Arabidopsisthaliana and rice genomes” Genome Biology. 7:R14; Nagaraju, J., et al.,(2002) “Genetic Analysis of Traditional and Evolved Basmati andNon-Basmati Rice Varieties by Using Fluorescence-based ISSR-PCR and SSRMarkers” Proc. Nat. Acad. Sci. USA. 99(9):5836-5841; and Lu, Hong, etal. (2005) “Population Structure and Breeding Patterns of 145 US RiceCultivars Based on SSR Marker Analysis” Crop Science. 45:66-76. Variousmolecular marker techniques may be used in combination to enhanceoverall resolution.

Rice DNA molecular marker linkage maps have been rapidly constructed andwidely implemented in genetic studies such as in Zhu, J. H., et al.(1999) “Toward rice genome scanning by map-based AFLP fingerprinting”Mol. Gene Genetics. 261(1):184-195; Cheng, Z., et al (2001) “Toward acytological characterization of the rice genome” Genome Research.11(12):2133-2141; Ahn, S., et al. (1993) “Comparative linkage maps ofthe rice and maize genomes” Proc. Natl. Acad. Sci. USA.90(17):7980-7984; and Kao, F. I., et al. (2006) “An integrated map ofOryza sativa L. chromosome 5” Theor. Appl. Genet. 112(5):891-902.Sequences and PCR conditions of SSR Loci in rice as well as the mostcurrent genetic map may be found in RiceBLAST and the TIGR Rice GenomeAnnotation on the World Wide Web.

One use of molecular markers is Quantitative Trait Loci (QTL) mapping.QTL mapping is the use of markers, which are known to be closely linkedto alleles that have measurable effects on a quantitative trait.Selection in the breeding process is based upon the accumulation ofmarkers linked to the positive effecting alleles and/or the eliminationof the markers linked to the negative effecting alleles from the plant'sgenome.

Molecular markers can also be used during the breeding process for theselection of qualitative traits. For example, markers closely linked toalleles or markers containing sequences within the actual alleles ofinterest can be used to select plants that contain the alleles ofinterest during a backcrossing breeding program. The markers can also beused to select for the genome of the recurrent parent and against thegenome of the donor parent. Using this procedure can minimize the amountof genome from the donor parent that remains in the selected plants. Itcan also be used to reduce the number of crosses back to the recurrentparent needed in a backcrossing program. The use of molecular markers inthe selection process is often called genetic marker enhanced selection.Molecular markers may also be used to identify and exclude certainsources of germplasm as parental varieties or ancestors of a plant byproviding a means of tracking genetic profiles through crosses.

Genes, Locus/Loci, Agronomic Traits, Foreign Protein Genes that can beUsed to Modify Hybrid Rice HR180001

Many agronomic genes as well as foreign protein genes can be transferredinto hybrid rice HR180001 that will express a specific phenotype or havean altered genetic component. More particularly, plants can begenetically engineered to express various phenotypes of agronomicinterest. Exemplary genes implicated in this regard include, but are notlimited to, those in the following categories:

1. Genes that Confer Resistance to Disease and Insects

A. Plant disease resistance genes. Plant defenses are often activated byspecific interaction between the product of a disease resistance gene(R) in the plant and the product of a corresponding avirulence (Avr)gene in the pathogen. A plant cultivar can be transformed with clonedresistance gene to engineer plants that are resistant to specificpathogen strains. See, for example Jones et al., Science 266:789 (1994)(cloning of the tomato Cf-9 gene for resistance to Cladosporium fulvum);Martin et al., Science 262:1432 (1993) (tomato Pto gene for resistanceto Pseudomonas syringae pv. tomato encodes a protein kinase); Mindrinoset al., Cell 78:1089 (1994) (Arabidopsis RSP2 gene for resistance toPseudomonas syringae); McDowell & Woffenden, (2003) Trends Biotechnol.21(4): 178-83 and Toyoda et al., (2002) Transgenic Res. 11 (6):567-82.

B. A Bacillus thuringiensis protein, a derivative thereof or a syntheticpolypeptide modeled thereon. See, for example, Geiser et al., Gene48:109 (1986), who disclose the cloning and nucleotide sequence of a Btδ-endotoxin gene. Moreover, DNA molecules encoding δ-endotoxin genes canbe purchased from American Type Culture Collection, Manassas, Va., forexample, under ATCC Accession Nos. 40098, 67136, 31995 and 31998.

C. A lectin. See, for example, the disclosure by Van Damme et al., PlantMolec. Biol. 24:25 (1994), who disclose the nucleotide sequences ofseveral Clivia miniata mannose-binding lectin genes.

D. A vitamin binding protein such as avidin. See PCT application US93/06487. The application teaches the use of avidin and avidinhomologues as larvicides against insect pests.

E. An enzyme inhibitor, for example, a protease or proteinase inhibitoror an amylase inhibitor. See, for example, Abe et al., J. Biol. Chem.262:16793 (1987) (nucleotide sequence of rice cysteine proteinaseinhibitor), Huub et al., Plant Molec. Biol. 21:985 (1993) (nucleotidesequence of cDNA encoding tobacco proteinase inhibitor I), Sumitani etal., Biosci. Biotech. Biochem. 57:1243 (1993) (nucleotide sequence ofStreptomyces nitrosporeus α-amylase inhibitor).

F. An insect specific hormone or pheromone such as an ecdysteroid andjuvenile hormone, a variant thereof, a mimetic based thereon, or anantagonist or agonist thereof. See, for example, the disclosure byHammock et al., Nature 344:458 (1990), of baculovirus expression ofcloned juvenile hormone esterase, an inactivator of juvenile hormone.

G. An insect specific peptide or neuropeptide which, upon expression,disrupts the physiology of the affected pest. For example, see thedisclosures of Regan, J. Biol. Chem. 269:9 (1994) (expression cloningyields DNA coding for insect diuretic hormone receptor), and Pratt etal., Biochem. Biophys. Res. Comm. 163:1243 (1989) (an allostatin isidentified in Diploptera puntata). Chattopadhyay et al. (2004) CriticalReviews in Microbiology 30 (1): 33-54 2004; Zjawiony (2004) J Nat Prod67 (2): 300-310; Carlini & Grossi-de-Sa (2002) Toxicon, 40 (11):1515-1539; Ussuf et al. (2001) Curr Sci. 80 (7): 847-853; andVasconcelos & Oliveira (2004) Toxicon 44 (4): 385-403. See also U.S.Pat. No. 5,266,317 to Tomalski et al., who disclose genes encodinginsect-specific, paralytic neurotoxins.

H. Insect specific venom produced in nature by a snake, a wasp, etc. Forexample, see Pang et al., Gene 116:165 (1992), for disclosure ofheterologous expression in plants of a gene coding for a scorpioninsectotoxic peptide.

I. An enzyme responsible for a hyper-accumulation of a monoterpene,sesquiterpene, steroid, a hydroxamic acid, a phenylpropanoid derivativeor another non-protein molecule with insecticidal activity.

J. An enzyme involved in the modification, including thepost-translational modification, of a biologically active molecule; forexample, a glycolytic enzyme, a proteolytic enzyme, a lipolytic enzyme,a nuclease, a cyclase, a transaminase, an esterase, a hydrolase, aphosphatase, a kinase, a phosphorylase, a polymerase, an elastase, achitinase and a glucanase, whether natural or synthetic. See PCTapplication WO 93/02197 in the name of Scott et al., which discloses thenucleotide sequence of a callase gene. DNA molecules which containchitinase-encoding sequences can be obtained, for example, from the ATCCunder Accession Nos. 39637 and 67152. See also Kramer et al., InsectBiochem. Molec. Biol. 23:691 (1993), who teach the nucleotide sequenceof a cDNA encoding tobacco hornworm chitinase, and Kawalleck et al.,Plant Molec. Biol. 21:673 (1993), who provide the nucleotide sequence ofthe parsley ubi4-2 polyubiquitin gene, U.S. Pat. Nos. 7,145,060,7,087,810 and 6,563,020.

K. A molecule that stimulates signal transduction. For example, see thedisclosure by Botella et al., Plant Molec. Biol. 24:757 (1994), ofnucleotide sequences for mung bean calmodulin cDNA clones, and Griess etal., Plant Physiol. 104:1467 (1994), who provide the nucleotide sequenceof a maize calmodulin cDNA clone.

L. A hydrophobic moment peptide. See PCT application WO 95/16776 andU.S. Pat. No. 5,580,852 which discloses peptide derivatives ofTachyplesin which inhibit fungal plant pathogens and PCT application WO95/18855 and U.S. Pat. No. 5,607,914 which teaches syntheticantimicrobial peptides that confer disease resistance, the respectivecontents of which are hereby incorporated by reference.

M. A membrane permease, a channel former or a channel blocker. Forexample, see the disclosure of Jaynes et al., Plant Sci 89:43 (1993), ofheterologous expression of a cecropin-β, lytic peptide analog to rendertransgenic tobacco plants resistant to Pseudomonas solanacearum.

N. A viral-invasive protein or a complex toxin derived therefrom. Forexample, the accumulation of viral coat proteins in transformed plantcells imparts resistance to viral infection and/or disease developmenteffected by the virus from which the coat protein gene is derived, aswell as by related viruses. See Beachy et al., Ann. Rev. Phytopathol.28:451 (1990). Coat protein-mediated resistance has been conferred upontransformed plants against alfalfa mosaic virus, cucumber mosaic virus,tobacco streak virus, potato virus X, potato virus Y, tobacco etchvirus, tobacco rattle virus and tobacco mosaic virus.

O. An insect-specific antibody or an immunotoxin derived therefrom.Thus, an antibody targeted to a critical metabolic function in theinsect gut would inactivate an affected enzyme, killing the insect. Cf.Taylor et al., Abstract #497, Seventh Intl Symposium on MolecularPlant-Microbe Interactions (Edinburgh, Scotland) (1994) (enzymaticinactivation in transgenic tobacco via production of single-chainantibody fragments).

P. A virus-specific antibody. See, for example, Tavladoraki et al.,Nature 366:469 (1993), who show that transgenic plants expressingrecombinant antibody genes are protected from virus attack.

Q. A developmental-arrestive protein produced in nature by a pathogen ora parasite. Thus, fungal endo-α-1, 4-D-polygalacturonases facilitatefungal colonization and plant nutrient release by solubilizing plantcell wall homo-α-1,4-D-galacturonase. See Lamb et al., Bio/Technology10:1436 (1992). The cloning and characterization of a gene which encodesa bean endopolygalacturonase-inhibiting protein is described by Toubartet al., Plant J. 2:367 (1992).

R. A developmental-arrestive protein produced in nature by a plant. Forexample, Logemann et al., Bio/Technology 10:305 (1992), have shown thattransgenic plants expressing the barley ribosome-inactivating gene havean increased resistance to fungal disease.

S. Genes involved in the Systemic Acquired Resistance (SAR) Responseand/or the pathogenesis-related genes. Briggs, S., Current Biology, 5(2)(1995); Pieterse & Van Loon (2004) Curr. Opin. Plant Bio. 7(4):456-64and Somssich (2003) Cell 113(7):815-6.

T. Antifungal genes. See Cornelissen and Melchers, Plant Physiol.,101:709-712 (1993); Parijs et al., Planta 183:258-264 (1991) andBushnell et al., Can. J. of Plant Path. 20(2):137-149 (1998). Also seeU.S. Pat. No. 6,875,907.

U. Detoxification genes, such as for fumonisin, beauvericin,moniliformin and zearalenone and their structurally related derivatives.For example, see U.S. Pat. No. 5,792,931.

V. Cystatin and cysteine proteinase inhibitors. See U.S. Pat. No.7,205,453.

W. Defensive genes. See WO 03/000863 and U.S. Pat. No. 6,911,577.

2. Genes that Confer Resistance to a Herbicide, for Example:

A. A herbicide that inhibits the growing point or meristem, such as animidazolinone or a sulfonylurea. Exemplary genes in this category codefor mutant ALS and AHAS enzyme as described, for example, by Lee et al.,EMBO J. 7:1241 (1988), and Miki et al., Theor. Appl. Genet. 80:449(1990), respectively.

B. Glyphosate resistance conferred by mutant5-enolpyruvlshikimate-3-phosphate synthase (EPSP) and aroA genes,respectively and other phosphono compounds such as glufosinate(phosphinothricin acetyl transferase (PAT) and Streptomyceshygroscopicus PAT bar genes), and pyridinoxy or phenoxy propionic acidsand cyclohexanediones (ACCase inhibitor-encoding genes). See, forexample, U.S. Pat. No. 4,940,835 to Shah, et al., which discloses thenucleotide sequence of a form of EPSP which can confer glyphosateresistance. U.S. Pat. No. 5,627,061 to Barry et al. also describes genesencoding EPSPS enzymes. See also U.S. Pat. Nos. 6,566,587; 6,338,961;6,248,876 B1; 6,040,497; 5,804,425; 5,633,435; 5,145,783; 4,971,908;5,312,910; 5,188,642; 4,940,835; 5,866,775; 6,225,114 B1; 6,130,366;5,310,667; 4,535,060; 4,769,061; 5,633,448; 5,510,471; Re. 36,449; RE37,287 E; and 5,491,288; and international publications EP1173580; WO01/66704; EP1173581 and EP1173582, which are incorporated herein byreference for this purpose. Glyphosate resistance is also imparted toplants that express a gene that encodes a glyphosate oxido-reductaseenzyme as described more fully in U.S. Pat. Nos. 5,776,760 and5,463,175, which are incorporated herein by reference for this purpose.In addition, glyphosate resistance can be imparted to plants by the overexpression of genes encoding glyphosate N-acetyltransferase. See, forexample, U.S. Pat. No. 7,462,481. A DNA molecule encoding a mutant aroAgene can be obtained under ATCC accession number 39256, and thenucleotide sequence of the mutant gene is disclosed in U.S. Pat. No.4,769,061 to Comai. European patent application No. 0 333 033 to Kumadaet al., and U.S. Pat. No. 4,975,374 to Goodman et al., disclosenucleotide sequences of glutamine synthetase genes which conferresistance to herbicides such as L-phosphinothricin. The nucleotidesequence of a PAT gene is provided in European Application No. 0 242 246to Leemans et al. DeGreef et al., Bio/Technology 7:61 (1989), describethe production of transgenic plants that express chimeric bar genescoding for PAT activity. Exemplary genes conferring resistance tophenoxy propionic acids and cyclohexanedione, such as sethoxydim andhaloxyfop are the Acc1-S1, Acc1-S2 and Acc1-S3 genes described byMarshall et al., Theor. Appl. Genet. 83:435 (1992).

C. A herbicide that inhibits photosynthesis, such as a triazine (psbAand gs+ genes) or a benzonitrile (nitrilase gene). Przibilla et al.,Plant Cell 3:169 (1991), describe the transformation of Chlamydomonaswith plasmids encoding mutant psbA genes. Nucleotide sequences fornitrilase genes are disclosed in U.S. Pat. No. 4,810,648 to Stalker, andDNA molecules containing these genes are available under ATCC AccessionNos. 53435, 67441, and 67442. Cloning and expression of DNA coding for aglutathione S-transferase is described by Hayes et al., Biochem. J.285:173 (1992).

3. Genes that Confer or Contribute to a Value-Added Trait, Such as:

A. Modified fatty acid metabolism, for example, by transforming a plantwith an antisense gene of stearyl-ACP desaturase to increase stearicacid content of the plant. See Knultzon et al., Proc. Natl. Acad. Sci.U.S.A. 89:2624 (1992).

B. Decreased phytate content, 1) Introduction of a phytase-encoding genewould enhance breakdown of phytate, adding more free phosphate to thetransformed plant. For example, see Van Hartingsveldt et al., Gene127:87 (1993), for a disclosure of the nucleotide sequence of anAspergillus niger phytase gene; 2) Up-regulation of a gene that reducesphytate content. In maize, this, for example, could be accomplished bycloning and then re-introducing DNA associated with one or more of thealleles, such as the LPA alleles identified in maize mutantscharacterized by low levels of phytic acid. See Raboy et al., Maydica35:383 (1990) and/or by altering inositol kinase activity as ininternational publication numbers WO 02/059324, WO 03/027243, WO99/05298, WO 2002/059324, WO 98/45448, WO 99/55882, WO 01/04147; U.S.Publication Numbers 2003/0009011, 2003/0079247; and U.S. Pat. Nos.6,197,561, 6,291,224, 6,391,348.

C. Modified carbohydrate composition affected, for example, bytransforming plants with a gene coding for an enzyme that alters thebranching pattern of starch or a gene altering thioredoxin such as NTRand/or TRX (See U.S. Pat. No. 6,531,648 which is incorporated byreference for this purpose) and/or a gamma zein knock out or mutant suchas cs27 or TUSC27 or en27 (See U.S. Pat. No. 6,858,778 and U.S.Publication Nos. 2005/0160488 and 2005/0204418, which are incorporatedby reference for this purpose). See Shiroza et al., J. Bacteol. 170:810(1988) (nucleotide sequence of Streptococcus mutannsfructosyltransferase gene), Steinmetz et al., Mol. Gen. Genet. 20:220(1985) (nucleotide sequence of Bacillus subtilis levansucrase gene), Penet al., Bio/Technology 10:292 (1992) (production of transgenic plantsthat express Bacillus licheniformis α-amylase), Elliot et al., PlantMolec. Biol. 21:515 (1993) (nucleotide sequences of tomato invertasegenes), Søgaard et al., J. Biol. Chem. 268:22480 (1993) (site-directedmutagenesis of barley α-amylase gene), and Fisher et al., Plant Physiol.102:1045 (1993) (maize endosperm starch branching enzyme II), WO99/10498 (improved digestibility and/or starch extraction throughmodification of UDP-D-xylose 4-epimerase, Fragile 1 and 2, Ref 1, HCHL,C4H), U.S. Pat. No. 6,232,529 (method of producing high oil seed bymodification of starch levels (AGP)). The fatty acid modification genesmentioned above may also be used to affect starch content and/orcomposition through the interrelationship of the starch and oilpathways.

D. Altering conjugated linolenic or linoleic acid content, such as ininternational publication number WO 01/12800. Altering LEC1, AGP, Dek1,Superal1, mi1ps, various Ipa genes such as Ipa1, Ipa3, hpt or hggt. Forexample, see international publication numbers WO 02/42424, WO 98/22604,WO 03/011015, WO 02/057439, WO 03/011015; U.S. Pat. Nos. 6,423,886,6,197,561, 6,825,397, 7,157,621; U.S. Publication No. 2003/0079247 andRivera-Madrid, R. et al. Proc. Natl. Acad. Sci. 92:5620-5624 (1995).

E. Altered antioxidant content or composition, such as alteration oftocopherol or tocotrienols. For example, see U.S. Pat. Nos. 6,787,683and 7,154,029 and international publication number WO 00/68393 involvingthe manipulation of antioxidant levels through alteration of a phytlprenyl transferase (ppt) and international publication number WO03/082899 through alteration of a homogentisate geranyl geranyltransferase (hggt).

F. Altered essential seed amino acids. For example, see U.S. Pat. No.6,127,600 (method of increasing accumulation of essential amino acids inseeds), U.S. Pat. No. 6,080,913 (binary methods of increasingaccumulation of essential amino acids in seeds), U.S. Pat. No. 5,990,389(high lysine), international publication number WO 99/40209 (alterationof amino acid compositions in seeds), international publication numberWO 99/29882 (methods for altering amino acid content of proteins), U.S.Pat. No. 5,850,016 (alteration of amino acid compositions in seeds),international publication number WO 98/20133 (proteins with enhancedlevels of essential amino acids), U.S. Pat. No. 5,885,802 (highmethionine), U.S. Pat. No. 5,885,801 (high threonine), U.S. Pat. No.6,664,445 (plant amino acid biosynthetic enzymes), U.S. Pat. No.6,459,019 (increased lysine and threonine), U.S. Pat. No. 6,441,274(plant tryptophan synthase beta subunit), U.S. Pat. No. 6,346,403(methionine metabolic enzymes), U.S. Pat. No. 5,939,599 (high sulphur),U.S. Pat. No. 5,912,414 (increased methionine), internationalpublication number WO 98/56935 (plant amino acid biosynthetic enzymes),international publication number WO 98/45458 (engineered seed proteinhaving higher percentage of essential amino acids), internationalpublication number WO 98/42831 (increased lysine), U.S. Pat. No.5,633,436 (increasing sulphur amino acid content), U.S. Pat. No.5,559,223 (synthetic storage proteins with defined structure containingprogrammable levels of essential amino acids for improvement of thenutritional value of plants), international publication number WO96/01905 (increased threonine), international publication number WO95/15392 (increased lysine), U.S. Pat. Nos. 6,930,225, 7,179,955,6,803,498, U.S. Publication No. 2004/0068767, international publicationnumbers WO 01/79516 and WO 00/09706 (Ces A: cellulose synthase), U.S.Pat. No. 6,194,638 (hemicellulose), U.S. Pat. Nos. 6,399,859 and7,098,381 (UDPGdH) and U.S. Pat. No. 6,194,638 (RGP).

4. Genes that Control Male Sterility

Male sterility genes can increase the efficiency with which hybrids aremade, in that they eliminate the need to physically emasculate the riceplant used as a female in a given cross. When one desires to employmale-sterility systems with a rice plant in accordance with theinvention, it may be beneficial to also utilize one or moremale-fertility restorer genes. For example, when cytoplasmic malesterility (CMS) is used, hybrid seed production requires three inbredlines: (1) a cytoplasmic male-sterile line having a CMS cytoplasm; (2) afertile inbred with normal cytoplasm, which is isogenic with the CMSline for nuclear genes (“maintainer line”); and (3) a distinct, fertileinbred with normal cytoplasm, carrying a fertility restoring gene(“restorer” line). The CMS line is propagated by pollination with themaintainer line, with all of the progeny being male sterile, as the CMScytoplasm is derived from the female parent. These male sterile plantscan then be efficiently employed as the female parent in hybrid crosseswith the restorer line, without the need for physical emasculation ofthe male reproductive parts of the female parent. The presence of amale-fertility restorer gene results in the production of fully fertileF1 hybrid progeny. If no restorer gene is present in the male parent,male-sterile hybrids are obtained. Such hybrids are useful when thevegetative tissue of the rice plant is utilized, but in most cases, theseeds will be deemed the most valuable portion of the crop, so fertilityof the hybrids in these crops must be restored. Therefore, one aspect ofthe current invention concerns the hybrid rice plant HR180001 comprisinga genetic locus capable of restoring male fertility in an otherwisemale-sterile plant.

There are several methods of conferring genetic male sterilityavailable, such as multiple mutant genes at separate locations withinthe genome that confer male sterility, as disclosed in U.S. Pat. Nos.4,654,465 and 4,727,219 to Brar et al., and chromosomal translocationsas described by Patterson in U.S. Pat. Nos. 3,861,709 and 3,710,511. Inaddition to these methods, Albertsen et al., U.S. Pat. No. 5,432,068,describes a system of nuclear male sterility which includes: identifyinga gene which is critical to male fertility; silencing this native genewhich is critical to male fertility; removing the native promoter fromthe essential male fertility gene and replacing it with an induciblepromoter; inserting this genetically engineered gene back into theplant; and thus creating a plant that is male sterile because theinducible promoter is not “on” resulting in the male fertility gene notbeing transcribed. Fertility is restored by inducing, or turning “on”,the promoter, which in turn allows the gene that, confers male fertilityto be transcribed.

A. A tapetum-specific gene, RTS, a rice anther-specific gene, isrequired for male fertility and its promoter sequence directstissue-specific gene expression in different plant species. Luo, Hong,et. al. (2006) Plant Molecular Biology. 62(3): 397-408(12). Introductionof a deacetylase gene under the control of a tapetum-specific promoterand with the application of the chemical N—Ac-PPT. See internationalpublication number WO 01/29237.

B. Introduction of various stamen-specific promoters. Riceanther-specific promoters which are of particular utility in theproduction of transgenic male-sterile monocots and plants for restoringtheir fertility. See U.S. Pat. No. 5,639,948. See also internationalpublications WO 92/13956 and WO 92/13957.

C. Introduction of the barnase and the barstar genes. See Paul et al.,(1992) Plant Mol. Biol. 19:611-622.

For additional examples of nuclear male and female sterility systems andgenes, see also, U.S. Pat. Nos. 5,859,341, 6,297,426, 5,478,369,5,824,524, 5,850,014 and 6,265,640. See also Hanson, Maureen R., et al.,(2004) “Interactions of Mitochondrial and Nuclear Genes That Affect MaleGametophyte Development” Plant Cell. 16: S154-S169, all of which arehereby incorporated by reference.

5. Genes that Affect Abiotic Stress Resistance

Genes that affect abiotic stress resistance (including but not limitedto flowering, panicle/glume and seed development, enhancement ofnitrogen utilization efficiency, altered nitrogen responsiveness,drought resistance or tolerance, cold resistance or tolerance, and saltresistance or tolerance) and increased yield under stress. For example,see: Xiong, Lizhong, et al., (2003) “Disease Resistance and AbioticStress Tolerance in Rice Are Inversely Modulated by an AbscisicAcid—Inducible Mitogen-Activated Protein Kinase” The Plant Cell.15:745-759, where OsMAPK5 can positively regulate drought, salt, andcold tolerance and negatively modulate PR gene expression andbroad-spectrum disease resistance in rice; Chen, Fang, et. al., (2006)“The Rice 14-3-3 Gene Family and its Involvement in Responses to Bioticand Abiotic Stress” DNA Research 13(2):53-63, where at least four riceGF14 genes, GF14b, GF14c, GF14e and Gf14f, were differentially regulatedby salinity, drought, wounding and abscisic acid; U.S. Publication No.2004/0148654 and International Publication No. WO 01/36596 whereabscisic acid is altered in plants resulting in improved plant phenotypesuch as increased yield and/or increased tolerance to abiotic stress;International Publication Nos. WO 2000/006341 and WO 04/090143, U.S.Publication No. 2004/0237147 and U.S. Pat. No. 6,992,237 where cytokininexpression is modified resulting in plants with increased stresstolerance, such as drought tolerance, and/or increased yield. Also, seeInternational Publication Nos. WO 02/02776, WO 2003/052063, WO 01/64898,JP2002281975 and U.S. Pat. Nos. 6,084,153, 6,177,275 and 6,107,547(enhancement of nitrogen utilization and altered nitrogenresponsiveness). For ethylene alteration, see U.S. Publication Nos.2004/0128719 and U.S 2003/0166197 and International Publication No. WO2000/32761. For plant transcription factors or transcriptionalregulators of abiotic stress, see e.g. U.S. Publication Nos.2004/0098764 and 2004/0078852.

Other genes and transcription factors that affect plant growth andagronomic traits such as yield, flowering, plant growth and/or plantstructure, can be introduced or introgressed into plants, see U.S. Pat.No. 6,573,430 (TFL), U.S. Pat. No. 6,713,663 (FT), U.S. Pat. Nos.6,794,560, 6,307,126 (GAI) and International Publication Nos. WO2004/076638 and WO 2004/031349 (transcription factors).

Genetic Complements

The development of hybrid rice involves three steps: (1) selectingplants from various germplasm pools; (2) selfing the selected plants forseveral generations to produce a series of inbred plants, which althoughdifferent from each other, each breed true and are highly uniform; and(3) crossing the selected inbred plants with unrelated inbred plants toproduce F1 hybrid progeny. During this inbreeding process in rice, thevigor of the plants may decrease; however, vigor is restored when twounrelated inbred plants are crossed to produce F1 hybrid progeny. Animportant consequence of the genetic homozygosity and homogeneity of aninbred plant is that the F1 hybrid progeny of any two inbred varietiesare genetically and phenotypically uniform. Plant breeders choose thesehybrid populations that display phenotypic uniformity. Once the inbredplants that produce superior hybrid progeny have been identified, theuniform traits of their hybrid progeny can be reproduced indefinitely aslong as the homogeneity of the inbred parents is maintained. Thedevelopment of inbred plants generally requires at least 5 to 7generations of selfing. Inbred plants are then cross-bred in an attemptto develop improved F1 hybrids. Hybrids are then screened and evaluatedfor adaptability for commercially important traits.

A hybrid rice plant characterized by molecular and physiological dataobtained from the representative sample of said hybrid rice depositedwith the American Type Culture Collection (ATCC), and a hybrid riceplant formed by the combination of the disclosed hybrid rice plant orplant cell with another rice plant or cell, are within the scope of thisdisclosure.

In addition to phenotypic observations, a plant can also be identifiedby its genotype. The genotype of a plant can be characterized through agenetic marker profile which can identify plants of the same variety ora related variety or be used to determine or validate a pedigree. Thepresent disclosure provides a genetic complement of the hybrid ricedesignated HR180001. As used herein, the phrase “genetic complement”means an aggregate of nucleotide sequences, the expression of whichdefines the phenotype of a rice plant or a cell or tissue of that plant.By way of example, a rice plant is genotyped to determine arepresentative sample of the inherited markers it possesses. Markers arealleles at a single locus. They are preferably inherited in codominantfashion so that the presence of both alleles at a diploid locus isreadily detectable, and they are free of environmental variation, i.e.,their heritability is 1. This genotyping is preferably performed on atleast one generation of the descendant plant for which the numericalvalue of the quantitative trait or traits of interest is alsodetermined. The array of single locus genotypes is expressed as aprofile of marker alleles, two at each locus. The marker alleliccomposition of each locus can be either homozygous or heterozygous.Homozygosity is a condition in which both alleles at a locus arecharacterized by the same nucleotide sequence or size of a repeatedsequence. Heterozygosity refers to different conditions of the gene at alocus. A preferred type of genetic marker for use with the invention isSingle Nucleotide Polymorphism (SNPs), although potentially any othertype of genetic marker could be used, for example, simple sequencerepeat (SSRs), restriction fragment length polymorphisms (RFLPs),amplified fragment length polymorphisms (AFLPs), and isozymes. Forexample, see Cregan et. al, “An Integrated Genetic Linkage Map of theSoybean Genome” Crop Science 39:1464-1490 (1999), and Berry et al.,Assessing Probability of Ancestry Using Simple Sequence Repeat Profiles:Applications to Maize Inbred Hybrids and Soybean Varieties” Genetics165:331-342 (2003), each of which are incorporated by reference hereinin their entirety.

Means of performing genetic marker profiles using SNP polymorphisms arewell known in the art. In addition, plants and plant parts substantiallybenefiting from the use of hybrid rice HR180001 in their development,such as hybrid rice HR180001 comprising a backcross conversion,transgene, or genetic sterility factor, may be identified by having amolecular marker profile with a high percent identity to hybrid riceHR180001. Such a percent identity might be 95%, 96%, 97%, 98%, 99%,99.5% or 99.9% identical to hybrid rice HR180001.

The marker profile of hybrid rice HR180001 also can be used to identifyessentially derived varieties and other progeny varieties developed fromthe use of hybrid rice HR180001, as well as cells and other plant partsthereof. Such plants may be developed using the markers identified ininternational publication number WO 00/31964, U.S. Pat. Nos. 6,162,967and 7,288,386. Progeny plants and plant parts produced using hybrid riceHR180001 may be identified by having a molecular marker profile with agenetic contribution from a rice hybrid or variety, as measured byeither percent identity or percent similarity. Such progeny may befurther characterized as being within a pedigree distance of hybrid riceHR180001, such as within 1, 2, 3, 4, or 5 or fewer cross-pollinations toa rice plant other than hybrid rice HR180001 or a plant that has hybridrice HR180001 as a progenitor.

While determining the genetic marker profile of the plants describedsupra, several unique marker profiles may also be identified which didnot appear in either parent of such rice plant. Such unique profiles mayarise during the breeding process from recombination or mutation. Acombination of several unique alleles provides a means of identifying aplant variety, an F1 progeny produced from such variety, and progenyproduced from such rice plants.

All of the compositions and methods disclosed and claimed herein can bemade and executed without undue experimentation in light of the presentdisclosure. While the compositions and methods have been described interms of the foregoing illustrative embodiments, it will be apparent tothose of skill in the art that variations, changes, modifications, andalterations may be applied to the composition, methods, and in the stepsor in the sequence of steps of the methods described herein withoutdeparting from the true concept, spirit, and scope of the disclosure.More specifically, it will be apparent that certain agents that are bothchemically and physiologically related may be substituted for the agentsdescribed herein while the same or similar results would be achieved.All such similar substitutes and modifications apparent to those skilledin the art are deemed to be within the spirit, scope, and concept of theinvention as defined by the appended claims.

DEPOSIT INFORMATION

A deposit of the hybrid rice seed HR180001 designated Accession No.PTA-125519 that is owned by RiceTec, Inc., was made with the AmericanType Culture Collection (ATCC) 10801 University Boulevard, Manassas, Va.20110 under the Budapest Treaty (37 CFR 1.801-1.809). The PTAcertificates cited are only issued after viability is confirmed. Thedate of deposit was Nov. 16, 2018. Access to this deposit will beavailable during the pendency of this application to persons determinedby the Commissioner of Patents and Trademarks to be entitled theretounder 37 CFR 1.14 and 35 USC 122. Upon allowance of any claims in thisapplication, all restrictions on the availability to the public of thehybrid will be irrevocably removed by affording access to a deposit ofat least 2,500 seeds of the same hybrid with the American Type CultureCollection, Manassas, Va.

The deposit will be maintained in the public repository for a period of30 years or 5 years after the last request or for the effective life ofthe patent, whichever is longer. The deposit will be replaced if itshould become inviable.

While a number of exemplary aspects and embodiments have been discussedabove, those of skill in the art will recognize certain modifications,permutations, additions and sub-combinations thereof. It is thereforeintended that the following appended claims and claims hereafterintroduced are interpreted to include all such modifications,permutations, additions and sub-combinations as are within their truespirit and scope.

What is claimed is:
 1. Hybrid rice seed HR180001, wherein arepresentative sample of seed was deposited under ATCC Accession No.PTA-125519.
 2. A rice plant, or a part thereof, produced by growing theseed of claim
 1. 3. Pollen or an ovule of the plant of claim
 2. 4. Atissue culture of cells produced from the plant of claim 2, wherein thecells of the tissue culture are produced from a plant part selected fromthe group consisting of leaves, pollen, embryos, cotyledon, hypocotyl,meristematic cells, roots, root tips, pistils, anthers, flowers, stems,glumes and panicles.
 5. A protoplast produced from the plant of claim 2.6. A protoplast produced from the tissue culture of claim
 4. 7. A riceplant regenerated from the tissue culture of claim 4, wherein the planthas the morphological and physiological characteristics of hybrid riceHR180001, as listed in Table
 1. 8. A method for producing a hybrid riceseed, wherein the method comprises crossing the plant of claim 2 with arice plant with a different genetic complement and harvesting theresultant hybrid rice seed.
 9. A method of producing a herbicideresistant rice plant, wherein the method comprises transforming the riceplant of claim 2 with a transgene, wherein the transgene conferstolerance to a herbicide selected from the group consisting ofimidazolinone, cyclohexanedione, sulfonylurea, glyphosate, glufosinate,phenoxy proprionic acid, isoxazole, triketone, L-phosphinothricin,triazine and benzonitrile.
 10. A method of producing an insect resistantrice plant, wherein the method comprises transforming the rice plant ofclaim 2 with a transgene that confers insect resistance.
 11. A method ofproducing a rice plant with modified fatty acid metabolism or modifiedcarbohydrate metabolism, wherein the method comprises transforming therice plant of claim 2 with a transgene encoding a protein selected fromthe group consisting of fructosyltransferase, levansucrase,alpha-amylase, invertase and starch branching enzyme and DNA encoding anantisense of stearyl-ACP desaturase.
 12. A method of introducing one ormore desired traits into hybrid rice designated HR180001, wherein themethod comprises: (a) crossing a hybrid rice HR180001 plant, from whicha representative sample of seed was deposited in the ATCC under theBudapest Treaty Accession No. PTA-125519, with a plant of another ricecultivar that comprises a desired trait, to produce progeny plants,wherein the desired trait(s) is selected from the group consisting ofmale sterility, herbicide resistance, insect resistance, modified fattyacid metabolism, modified carbohydrate metabolism, and resistance tobacterial disease, fungal disease and viral disease; (b) selecting oneor more progeny plants that have the desired trait(s) to produceselected progeny plants; (c) backcrossing the selected progeny plantswith the HR180001 plants; (d) selecting for backcross progeny plantsthat have the desired trait(s); and (e) repeating steps (c) and (d)three or more times to produce selected fourth or higher backcrossprogeny plants that comprise the desired trait(s).
 13. A plant producedby the method of claim 12, wherein the plant has the desired trait(s)and the physiological and morphological characteristics of hybrid riceHR180001 as listed in Table
 1. 14. A method of growing a blend of riceseed, wherein the method comprises: a) planting a blend comprising afirst quantity of rice seed of claim 1 mixed with a second quantity ofrice seed of another rice variety, rice hybrid or rice inbred; b)growing said seeds to produce rice plants; c) allowing cross pollinationto occur between plants from first quantity of seed and plants fromsecond quantity of seed; and d) harvesting seeds from the crossing ofsaid rice plants.
 15. The method of claim 14, wherein the blend furthercomprises seeds from a third, fourth or fifth rice variety, rice hybridor rice inbred.
 16. The method of claim 15, wherein the blend iscomprised of about 1% to about 95% of hybrid rice HR180001 seed.
 17. Amethod of producing a blend of rice seed, wherein the method comprises:a) providing a first quantity of rice seed of claim 1; b) providing asecond quantity of rice seed of another rice variety, rice inbred orrice hybrid; and c) producing a blend comprised of mixing said firstquantity of rice seed with said second quantity of rice seed.
 18. Themethod of claim 17, wherein said blend is comprised of about 1% to about95% of hybrid rice HR180001 seed.